Ribozymes, 2 Volume Set Principles, Methods, Applications

Provides comprehensive coverage of a core field in the molecular biosciences, bringing together decades of knowledge from the world?s top professionals in the field

Timely and unique in its breadth of content, this all-encompassing and authoritative reference on ribozymes documents the great diversity of nucleic acid-based catalysis. It integrates the knowledge gained over the past 35 years in the field and features contributions from virtually every leading expert on the subject.

Ribozymes is organized into six major parts. It starts by describing general principles and strategies of nucleic acid catalysis. It then introduces naturally occurring ribozymes and includes the search for new catalytic motifs or novel genomic locations of known motifs. Next, it covers the development and design of engineered ribozymes, before moving on to DNAzymes as a close relative of ribozymes. The next part examines the use of ribozymes for medicinal and environmental diagnostics, as well as for therapeutic tools. It finishes with a look at the tools and methods in ribozyme research, including the techniques and assays for structural and functional characterization of nucleic acid catalysts.

• The first reference to tie together all aspects of the multi-faceted field of ribozymes
• Features more than 30 comprehensive chapters in two volumes
• Covers the chemical principles of RNA catalysis; naturally occurring ribozymes, engineered ribozymes; DNAzymes; ribozymes as tools in diagnostics and therapy, and tools and methods to study ribozymes
• Includes first-hand accounts of concepts, techniques, and applications by a team of top international experts from leading academic institutions
• Dedicates half of its content to methods and practical applications, ranging from bioanalytical tools to medical diagnostics to therapeutics

Ribozymes is an unmatched resource for all biochemists, biotechnologists, molecular biologists, and bioengineers interested in the topic.

Volume 1

Preface xvii

Foreword xix

Part I Nucleic Acid Catalysis: Principles, Strategies and Biological Function 1

1 The Chemical Principles of RNA Catalysis 3
Timothy J. Wilson and David M. J. Lilley

1.1 RNA Catalysis 3

1.2 Rates of Chemical Reactions and Transition State Theory 4

1.3 Phosphoryl Transfer Reactions in the Ribozymes 5

1.4 Catalysis of Phosphoryl Transfer 6

1.5 General Acid–Base Catalysis in Nucleolytic Ribozymes 8

1.5.1 The Fraction of Active Catalyst, and the pH Dependence of Reaction Rates 9

1.5.2 The Reactivity of General Acids and Bases 13

1.6 pK_a Shifting of General Acids and Bases in Nucleolytic Ribozymes 13

1.7 Catalytic Roles of Metal Ions in Ribozymes 14

1.8 The Choice Between General Acid–Base Catalysis and the Use of Metal Ions 17

1.9 The Limitations to RNA Catalysis 18

Acknowledgment 18

References 19

2 Biological Roles of Self-Cleaving Ribozymes 23
Christina E. Weinberg

2.1 Introduction 23

2.2 Use of Self-cleaving Ribozymes for Replication 25

2.2.1 Viroids 25

2.2.2 Viroid-like Satellite RNAs 28

2.2.3 Hepatitis δ Virus RNA 29

2.2.4 Neurospora Varkud Satellite RNAs Replicate Using a DNA Intermediate 29

2.3 Self-cleaving Ribozymes as Part of Transposable Elements 30

2.3.1 R2 Elements: Non-LTR Retrotransposons that Use HDV-like Ribozymes for Retrotransposition 30

2.3.2 HDV-like Ribozymes in Other Non-LTR Retrotransposon Lineages 34

2.3.3 Penelope-like Elements (PLEs) Contain Hammerhead Ribozymes 35

2.3.4 Hammerhead Ribozymes Associated with Repetitive Elements in Schistosoma mansoni 39

2.3.5 Retrozymes: A New Class of Plant Retrotransposons that Contains Hammerhead Ribozymes 40

2.4 Hammerhead Ribozymes with Suggested Roles in mRNA Biogenesis 41

2.5 The glmS Ribozyme Regulates Glucosamine-6-phosphate Levels in Bacteria 41

2.6 The Biological Roles of Many Ribozymes Are Unknown 42

2.7 Conclusion 43

Acknowledgments 43

References 44

Part II Naturally Occurring Ribozymes 55

3 Chemical Mechanisms of the Nucleolytic Ribozymes 57
Timothy J. Wilson and David M. J. Lilley

3.1 The Nucleolytic Ribozymes 57

3.2 Some Nucleolytic Ribozymes AreWidespread 58

3.3 Secondary Structures of Nucleolytic Ribozymes – Junctions and Pseudoknots 58

3.4 Catalytic Players in the Nucleolytic Ribozymes 60

3.5 The Hairpin and VS Ribozymes: The G Plus A Mechanism 61

3.6 The Twister Ribozyme: A G Plus A Variant 66

3.7 The Hammerhead Ribozyme: A 2′-Hydroxyl as a Catalytic Participant 69

3.8 The Hepatitis Delta Virus Ribozyme: A Direct Role for a Metal Ion 72

3.9 The Twister Sister (TS) Ribozyme: Another Metallo-Ribozyme 74

3.10 The Pistol Ribozyme: A Metal Ion as the General Acid 76

3.11 The glmS Ribozyme: Participation of a Coenzyme 78

3.12 A Classification of the Nucleolytic Ribozymes Based on Catalytic Mechanism 79

Acknowledgments 83

References 83

4 TheglmS Ribozyme and Its Multifunctional Coenzyme Glucosamine-6-phosphate 91
Juliane Soukup

4.1 Introduction 91

4.2 Ribozymes 91

4.3 Riboswitches 92

4.4 The glmS Riboswitch/Ribozyme 93

4.5 Biological Function of the glmS Ribozyme 94

4.6 glmS Ribozyme Structure and Function – Initial Biochemical Analyses 95

4.7 glmS Ribozyme Structure and Function – Initial Crystallographic Analysis 98

4.8 Metal Ion Usage by the glmS Ribozyme 99

4.9 In Vitro Selected glmS Catalyst Loses Coenzyme Dependence 101

4.10 Essential Coenzyme GlcN6P Functional Groups 102

4.11 Mechanism of glmS Ribozyme Self-Cleavage 104

4.11.1 Importance of Coenzyme GlcN6P 104

4.11.2 pH-Reactivity Profiles 106

4.11.3 Role of an Active Site Guanine 108

4.12 Potential for Antibiotic Development Affecting glmS Ribozyme/Riboswitch Function 109

Acknowledgments 110

References 110

5 The Lariat Capping Ribozyme 117
Henrik Nielsen, Nicolai Krogh, Benoît Masquida, and Steinar Daae Johansen

5.1 Introduction 117

5.1.1 The Basics 117

5.1.2 A Brief Account of the Discovery of the Lariat Capping Ribozyme 119

5.1.3 Readers Guide to Nomenclature 120

5.1.4 The Species Involved 120

5.2 Reactions Catalyzed by LCrz 121

5.2.1 The Branching Reaction 122

5.2.2 Ligation and Hydrolysis 122

5.2.3 Reaction Conditions 124

5.3 The Structure of the LCrz Core 125

5.3.1 The Detailed Structure of DirLCrz 125

5.3.2 Structure of the Naegleria-type LCrz 126

5.4 Communication Between LCrz and Flanking Elements 128

5.4.1 Group I Ribozyme Switching 128

5.4.2 LC Ribozyme Switching 130

5.4.3 A Role of Spliceosomal Intron I51 in DirLCrz Regulation? 131

5.5 Reflections on the Evolutionary Aspect of LCrz 131

5.5.1 A Model for the Emergence of LCrz 132

5.5.2 An Evolutionary Path to Spliceosomal Splicing? 132

5.6 LCrz as a Research Tool 134

5.7 Conclusions and Unsolved Problems 136

References 138

6 Self-Splicing Group II Introns 143
Isabel Chillón and Marco Marcia

6.1 Introduction 143

6.2 Milestones in the Characterization of Group II Introns 143

6.3 Evolutionary Conservation and Biological Role 145

6.3.1 Phylogenetic Classifications 145

6.3.2 Differentiation and Evolutionarily Acquired Properties 148

6.3.3 Spreading and Survival in the Host Genome 149

6.4 Structural Architecture 152

6.4.1 Secondary Structure and Long-Range Tertiary Interactions 152

6.4.2 Folding 153

6.4.3 Stabilization by Solvent and IEP 154

6.4.4 Active Site and Reaction Mechanism 154

6.5 Lessons and Tools from Group II Intron Research 156

6.5.1 Analogies to Other Splicing Machineries 156

6.5.2 Lessons to Study Other Large Non-coding RNAs 157

6.5.3 Biotechnological Applications of GIIi 157

6.6 Perspectives and Open Questions 158

Acknowledgments 158

References 158

7 The Spliceosome: an RNA–Protein Ribozyme Derived From Ancient Mobile Genetic Elements 169
Erin L. Garside, Oliver A. Kent, and Andrew M. MacMillan

7.1 Discovery of Introns and Splicing 169

7.2 snRNPs and the Spliceosome 170

7.3 The Spliceosomal Cycle 171

7.4 Chemistry of Splicing 173

7.5 Spliceosome Structural Analysis 177

7.6 Spliceosome Structures 177

7.6.1 Pre-spliceosome: Tri-snRNP 177

7.6.2 Pre-spliceosome: A Complex 179

7.6.3 B Complex 179

7.6.4 Activated B Complex 182

7.6.5 C and C* Complexes 183

7.6.6 P Complex 185

7.6.7 Intron Lariat Spliceosome Complex 185

7.7 Insights from Spliceosome Disassembly 187

7.8 Conservation of Spliceosomal and Group II Active Sites 187

7.9 Summary and Perspectives 188

References 189

8 The Ribosome and Protein Synthesis 193
Paul Huter, Michael Graf, and Daniel N. Wilson

8.1 Central Dogma of Molecular Biology 193

8.2 Structure of the E. coli Ribosome 194

8.3 Translation Cycle 194

8.3.1 Initiation 196

8.3.2 Elongation 199

8.3.3 Termination 208

8.3.4 Recycling 211

References 213

9 The RNase P Ribozyme 227
Markus Gößringer, Isabell Schencking, and Roland Karl Hartmann

9.1 Introduction 227

9.2 Bacterial RNase P 229

9.2.1 P RNA Structure and Evolution 229

9.2.2 The Single Protein Subunit 233

9.2.3 P RNAs – Architectural Principles, Variations, Idiosyncrasies 233

9.3 Substrate Interaction 235

9.4 RNA-based Metal Ion Catalysis 247

9.4.1 The Two-metal Ion Mechanism 247

9.4.2 Architecture of the Active Site 250

9.4.3 The “A248/nt −1” Interaction 251

9.4.4 Specific RNase P Cleavage by the P15 Module 253

9.5 RNase P as an Antibiotic Target 254

9.5.1 P RNA as a Target 254

9.5.2 The Bacterial RNase P Holoenzyme as Target 257

9.5.3 P Protein as a Target 258

9.6 Application of RNase P as a Tool in Gene Inactivation 258

9.6.1 The Guide Sequence (GS) Concept 258

9.6.2 EGS Technology in Eukaryotic Cells 259

9.6.3 EGS Oligonucleotides and Recruitment of Human Nuclear-Cytoplasmic RNase P 261

9.6.4 The M1–GS Approach 265

9.6.5 Outlook 266

References 267

10 Ribozyme Discovery in Bacteria 281
Adam Roth and Ronald Breaker

10.1 Introduction 281

10.2 Protein Takeover 282

10.3 Ribozymes as Evolutionary Holdouts 282

10.4 The Role of Serendipity in Early Ribozyme Discoveries 283

10.5 Ribozymes Emerge from Structured Noncoding RNA Searches 285

10.6 Ribozymes Beget Ribozymes 289

10.7 Ribozyme Dispersal Driven by Association with Selfish Elements 291

10.8 Domesticated Ribozymes 292

10.9 New Ribozymes from Old 294

10.10 Will New ncRNAs Broaden the Scope of RNA Catalysis? 295

Acknowledgments 296

References 296

11 Small Self-Cleaving Ribozymes in the Genomes of Vertebrates 303
Marcos de la Peña

11.1 The Family of Small Self-Cleaving Ribozymes in Eukaryotic Genomes: From Retrotransposition to Domestication 303

11.2 The Widespread Case of the Hammerhead Ribozyme: From Bacteria to Vertebrate Genomes 304

11.2.1 The Discontinuous HHR in Mammals 307

11.2.2 Intronic HHRs in Amniotes 310

11.3 Other Intronic HHRs in Amniotes: Small Catalytic RNAs in Search of a Function 315

11.4 The Family of the Hepatitis D Virus Ribozymes 318

11.4.1 An Intronic HDV-Like Ribozyme Conserved in the Genome of Mammals 320

11.5 Other Small Self-Cleaving Ribozymes Hidden in the Genomes of Vertebrates? 322

References 323

Part III Engineered Ribozymes 329

12 Phosphoryl Transfer Ribozymes 331
Razvan Cojocaru and Peter J. Unrau

12.1 Introduction 331

12.2 Kinase Ribozymes 332

12.3 Glycosidic Bond Forming Ribozymes 336

12.4 Capping Ribozymes 340

12.5 Ligase Ribozymes 344

12.6 Polymerase Ribozymes 351

12.7 Summary 353

References 353

13 RNA Replication and the RNA Polymerase Ribozyme 359
Falk Wachowius and Philipp Holliger

13.1 Introduction 359

13.2 Nonenzymatic RNA Polymerization 360

13.3 Enzymatic RNA Polymerization 361

13.4 Essential Requirements for an RNA Replicator 363

13.4.1 Likelihood of Replicating Sequences in RNA Sequence Space 364

13.4.2 Reaction Conditions for RNA Replication 366

13.4.3 The Strand Separation Problem 367

13.5 The Class I Ligase and the First RNA Polymerase Ribozymes 367

13.6 Structural Insight into the Catalytic Core of the RNA Polymerase Ribozyme 372

13.7 Selection for Improved Polymerase Activity I 374

13.8 Selection for Improved Polymerase Activity II 377

13.9 Conclusion and Outlook 380

References 381

14 Maintenance of Genetic Information in the First Ribocell 387
Ádám Kun

14.1 The Ribocell and the Stages of the RNAWorld 387

14.1.1 Replication of the Genetic Information 389

14.1.2 On the Metabolic Complexity of Ribocells 389

14.2 The Error Thresholds 391

14.2.1 Introducing the Error Threshold 391

14.2.2 The Fitness Landscape and Neutrality of Mutations 393

14.3 Compartmentalization 396

14.3.1 Surface Metabolism and Transient Compartmentalization 397

14.3.2 The Stochastic Corrector Model 399

14.4 Minimal Gene Content of the First Ribocell 401

14.4.1 Intermediate Metabolism 402

14.4.2 Cell-Level Processes 404

Acknowledgments 406

References 406

15 Ribozyme-Catalyzed RNA Recombination 419
Benedict A. Smail and Niles Lehman

15.1 Introduction 419

15.2 RNA Recombination Chemistry 420

15.3 Azoarcus Group I Intron 421

15.4 Crystal Structure 422

15.5 Mechanism 422

15.6 Model for Prebiotic Chemistry 423

15.7 Spontaneous Self-assembly of Azoarcus RNA Fragments 425

15.8 Autocatalysis 428

15.9 Cooperative Self-assembly 429

15.10 Game Theoretic Treatment 430

15.11 Significance of Game Theoretic Treatments 432

15.12 Other Recombinase Ribozymes 433

15.13 Conclusions 435

References 436

16 Engineering of Hairpin Ribozymes for RNA Processing Reactions 439
Robert Hieronymus, Jikang Zhu, Bettina Appel, and Sabine Müller

16.1 Introduction 439

16.2 The Naturally Occurring Hairpin Ribozyme 440

16.3 Structural Variants of the Hairpin Ribozyme 442

16.4 Hairpin Ribozymes that are Regulated by External Effectors 443

16.5 Twin Ribozymes for RNA Repair and Recombination 446

16.6 Hairpin Ribozymes as RNA Recombinases 449

16.7 Self-Splicing Hairpin Ribozymes 452

16.8 Closing Remarks 454

References 456

17 Engineering of the Neurospora Varkud Satellite Ribozyme for Cleavage of Nonnatural Stem-Loop Substrates 463
Pierre Dagenais, Julie Lacroix-Labonté, Nicolas Girard, and Pascale Legault

17.1 Introduction 463

17.2 Simple Primary and Secondary Structure Changes Compatible with Substrate Cleavage by the VS Ribozyme 464

17.2.1 Circular Permutations and trans Cleavage 464

17.2.2 The I/V Kissing-Loop Interaction and the Associated Conformational Change in SLI 466

17.2.3 Summary of SLI Sequences Compatible with Cleavage by the Wild-Type VS Ribozyme 468

17.3 The Structural Context 470

17.3.1 NMR Investigations of the VS Ribozyme 470

17.3.2 Crystal Structures of a Dimeric Form of the VS Ribozyme 473

17.3.3 Open and Closed States of the S/R Complex 473

17.4 Structure-Guided Engineering Studies 474

17.4.1 Helix-Length Compensation 474

17.4.2 Kissing-Loop Substitutions 475

17.4.3 Role of KLI Dynamics in the Cleavage Reaction 476

17.4.4 Improving the Cleavage Activity of a Designer Ribozyme 478

17.5 Summary and Future Prospects for VS Ribozyme Engineering 480

References 481

18 Chemical Modifications in Natural and Engineered Ribozymes 487
Stephanie Kath-Schorr

18.1 Introduction 487

18.2 Chemical Modifications to Study Natural Ribozymes 488

18.2.1 Modified Nucleotides for Mechanistic and Structural Studies on Ribozymes 488

18.2.2 Stabilization of Ribozymes by Chemical Modifications for in Cell Applications 489

18.3 In Vitro Selection with Chemically Modified Nucleotides: Expanding the Scope of DNA and RNA Catalysis 490

18.3.1 General Aspects for In Vitro Selection Using Unnatural Nucleotides 491

18.3.2 Selection of Deoxyribozymes with Modified Nucleotides 492

18.3.3 Artificial Ribozymes with Nonnatural Nucleobases 494

18.3.4 Catalysts With Nonnatural Backbones: XNAzymes 495

18.4 Outlook 495

References 496

19 Ribozymes for Regulation of Gene Expression 505
Julia Stifel and Jörg S. Hartig

19.1 Introduction 505

19.2 Conditional Gene Expression Control by Riboswitches 505

19.3 Allosteric Ribozymes as Engineered Riboswitches 506

19.4 In Vitro Selection Methods 507

19.5 In Vivo Screening Methods 508

19.6 Rational Design of Allosteric Ribozymes 511

19.7 Applications of Aptazymes for Gene Regulation 512

References 514

20 Development of Flexizyme Aminoacylation Ribozymes and Their Applications 519
Takayuki Katoh, Yuki Goto, Toby Passioura, and Hiroaki Suga

20.1 Introduction 519

20.2 The First Ribozymes Catalyzing Acyl Transfer to RNAs 520

20.3 The ATRib Variant Family: Ribozymes Catalyzing tRNA Aminoacylation via Self-Acylated Intermediates 521

20.4 Prototype Flexizymes: Ribozymes Catalyzing Direct tRNA Aminoacylation 523

20.5 Flexizymes: Versatile Ribozymes for the Preparation of Aminoacyl-tRNAs 526

20.6 Application of Flexizymes to Genetic Code Reprogramming 527

20.7 Development of Orthogonal tRNA/Ribosome Pairs Using Mutant Flexizymes 530

20.8 In Vitro Selection of Bioactive Peptides Containing nPAAs Through RaPID Display 532

20.9 tRid: A Method for Selective Removal of tRNAs from an RNA Pool 535

20.10 Use of a Natural Small RNA Library Lacking tRNA for In Vitro Selection of a Folic Acid Aptamer: Small RNA Transcriptomic SELEX 535

20.11 Summary and Perspective 537

Acknowledgments 539

References 539

21 In Vitro Selected (Deoxy)ribozymes that Catalyze Carbon–Carbon Bond Formation 545
Michael Famulok

21.1 Introduction 545

21.2 Diels–Alderase Ribozymes 546

21.3 Aldolase Ribozyme 547

21.4 A DNAzyme that Catalyzes a Friedel–Crafts Reaction 548

21.5 Alkylating Ribozymes 550

21.6 Conclusion 554

References 555

22 Nucleic Acid-Catalyzed RNA Ligation and Labeling 557
Mohammad Ghaem Maghami and Claudia Höbartner

22.1 Introduction 557

22.2 Ribozymes for RNA Labeling at Internal Positions 558

22.2.1 Fluorescein Iodoacetamide Reactive Ribozyme 558

22.2.2 Genomically Derived Epoxide Reactive Ribozyme 559

22.2.3 Twin Ribozyme 561

22.2.4 DNA as a Catalyst for Ligation of Modified RNA 562

22.2.5 Site-Specific Internal Labeling of RNA with DNA Enzymes 563

22.3 RNA-Catalyzed Labeling of RNA at the 3′-end 564

22.4 Potential Ribozymes for RNA Labeling at the 5′-end 565

22.5 Conclusions 566

Acknowledgments 566

References 568

Volume 2

Preface xiii

Foreword xv

Part IV DNAzymes 571

23 The Chemical Repertoire of DNA Enzymes 573
Marcel Hollenstein

24 Light-Utilizing DNAzymes 621
Adam Barlev and Dipankar Sen

25 Diverse Applications of DNAzymes in Computing and Nanotechnology 633
Matthew R. Lakin, Darko Stefanovic, and Milan N. Stojanovic

Part V Ribozymes/DNAzymes in Diagnostics and Therapy 661

26 Optimization of Antiviral Ribozymes 663
Alfredo Berzal-Herranz and Cristina Romero-López

27 DNAzymes as Biosensors 685
Lingzi Ma and Juewen Liu

28 Compartmentalization-Based Technologies for In Vitro Selection and Evolution of Ribozymes and Light-Up RNA Aptamers 721
Farah Bouhedda and Michael Ryckelynck

Part VI Tools and Methods to Study Ribozymes 739

29 Elucidation of Ribozyme Mechanisms at the Example of the Pistol Ribozyme 741
Christoph Falschlunger, Josef Leiter, and Ronald Micura

30 Strategies for Crystallization of Natural Ribozymes 753
Benoît Masquida, Diana Sibrikova, and Maria Costa

31 NMR Spectroscopic Investigation of Ribozymes 785
Bozana Knezic, Oliver Binas, Albrecht Eduard Völklein, and Harald Schwalbe

32 Studying Ribozymes with Electron Paramagnetic Resonance Spectroscopy 817
Olav Schiemann

33 Computational Modeling Methods for 3D Structure Prediction of Ribozymes 861
Pritha Ghosh, Chandran Nithin, Astha Joshi, Filip Stefaniak, Tomasz K. Wirecki, and Janusz M. Bujnicki

Index 883

Sabine Müller is Full Professor for Biochemistry/Bioorganic Chemistry at University Greifswald (Germany), and is a member of the Leibniz-Sozietät der Wissenschaften zu Berlin and of AcademiaNet. She has been working in the field of RNA engineering and has made important contributions to ribozyme research.

Benoît Masquida is a Research Director at Centre National de la Recherche Scientifique, and carries on research and teaching activities at the University of Strasbourg (France). He made important contributions in the field of RNA structural biology, notably through identification of new RNA folds and their evolutionary relationships.

Wade Winkler is Professor of Cell Biology and Molecular Genetics at the University of Maryland (USA), and has authored multiple influential publications on the different types of regulatory RNAs in bacteria.